Stampy on 454

[colindaven]

I've been using Stampy to map Illumina reads and it's great. However I'd like to use it for 454 alignment too so as to get SAM output, which is a better match to our SNP calling pipelines than the 454HCDiffs and .tsvs generated by Newbler.

However, Stampy only manages to map about 48% of 310000 reads, as opposed to Newbler mapping over 85%.

Has anyone else tried to modify settings on Stampy to better map 454 data ? Or has any other recommendations for getting 454 data mapped in SAM format ?

cheers
Colin

[nickloman]

Generally speaking I don't recommend people use software optimised for short-reads on 454 data. That is because the error model is quite different (454 reads contain plenty of indels not usually seen with Illumina data) and the algorithm trades speed for sensitivity, e.g. by k-mer matching, whereas 454 reads are longer and fewer and can usually be successfully aligned with a slower and more accurate algorithm.

Your options include:
- Use gsMapper and convert output to SAM using glu-genetics Newbler2SAM. I have successfully done this.
- Use a mapper which is optimised for 454 data. Options include LASTZ, BWASW, Novoalign, SSAHA2. See http://seqanswers.com/forums/showthread.php?t=1229

[shaojingwang]

perhaps, gmap could met your needs, see http://www.gene.com/share/gmap/src/g...7-09-28.tar.gz

[lh3]

Bowtie2, bwa-sw and smalt